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Yorodumi- PDB-5y6l: A subcomplex crystal structure of human cytosolic aspartyl-tRNA s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y6l | ||||||
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Title | A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex | ||||||
Components |
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Keywords | LIGASE / AMINO-ACYL TRNA SYNTHETASE COMPLEX / MULTI-SYNTHETASE COMPLEX / LIGATION AMINO ACID TO TRNA | ||||||
Function / homology | Function and homology information type II pneumocyte differentiation / aminoacylase activity / aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / positive regulation of DNA damage response, signal transduction by p53 class mediator / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity ...type II pneumocyte differentiation / aminoacylase activity / aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / regulation of long-chain fatty acid import into cell / aspartate-tRNA ligase activity / positive regulation of DNA damage response, signal transduction by p53 class mediator / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / RNA stem-loop binding / GAIT complex / cellular response to platelet-derived growth factor stimulus / rRNA transcription / positive regulation of apoptotic signaling pathway / cellular response to epidermal growth factor stimulus / cellular response to leukemia inhibitory factor / positive regulation of protein ubiquitination / cellular response to type II interferon / cellular response to insulin stimulus / positive regulation of cellular senescence / GTPase binding / protein-containing complex assembly / tRNA binding / negative regulation of translation / molecular adaptor activity / protein ubiquitination / ribonucleoprotein complex / translation / positive regulation of apoptotic process / negative regulation of cell population proliferation / synapse / apoptotic process / nucleolus / protein homodimerization activity / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Cho, H.Y. / Lee, H.J. / Kang, B.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To be published Title: A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex Authors: Cho, H.Y. / Lee, H.J. / Kang, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y6l.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y6l.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 5y6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/5y6l ftp://data.pdbj.org/pub/pdb/validation_reports/y6/5y6l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 25956.354 Da / Num. of mol.: 1 / Fragment: UNP residues 1-224, MRS N-TERMINUS DOMAIN / Mutation: S171R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MARS / Production host: Escherichia coli (E. coli) / References: UniProt: P56192, methionine-tRNA ligase |
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#2: Protein | Mass: 21226.016 Da / Num. of mol.: 1 Fragment: AIMP3 WITH ADDITIONAL S SEQUENCE AT THE N-TERMINUS Mutation: C147S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1E1, AIMP3, P18 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43324 |
#3: Protein | Mass: 19310.699 Da / Num. of mol.: 1 / Fragment: UNP residues 1-175, EPRS GST-LIKE DOMAIN / Mutation: C92S, C105S, C123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli) / References: UniProt: P07814, glutamate-tRNA ligase |
#4: Protein | Mass: 26790.916 Da / Num. of mol.: 1 / Fragment: UNP residues 90-320, AIMP2 GST-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIMP2, JTV1, PRO0992 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13155 |
#5: Protein | Mass: 59384.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DARS, PIG40 / Production host: Escherichia coli (E. coli) / References: UniProt: P14868, aspartate-tRNA ligase |
-Non-polymers , 2 types, 80 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 3000 Na/K phosphate pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 24317 / % possible obs: 99.5 % / Redundancy: 6.8 % / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2376 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BVY, 5BMU, 5A34 Resolution: 2.9→29.873 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→29.873 Å
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Refine LS restraints |
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LS refinement shell |
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